chr13-33016046-G-A

Position:

• chr13-33016046-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047430819.1(LOC124903151):​c.397C>T​(p.Pro133Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,232 control chromosomes in the GnomAD database, including 2,381 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.17 (2381 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LOC124903151 XM_047430819.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

LOC124903151 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903151	XM_047430819.1	c.397C>T	p.Pro133Ser	missense_variant	1/2		XP_047286775.1
LOC124903151	XR_007063749.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25965 AN: 152114 Hom.: 2377 Cov.: 33

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.167

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.171 AC: 25972 AN: 152232 Hom.: 2381 Cov.: 33 AF XY: 0.172 AC XY: 12832 AN XY: 74414

Gnomad4 AFR AF: 0.0927

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.165

Alfa AF: 0.178 Hom.: 507

Bravo AF: 0.168

Asia WGS AF: 0.177 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.6
DANN	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1207568; hg19: chr13-33590184;